Computational Biophysics Workshop - Urbana, Nov. 18-22, 2013
Laptop Setup
This page describes how workshop participants should set up their laptops for participation in workshop hands-on tutorial sessions.
I. Install Software
Tutorial sessions use the VMD - version 1.9.1 and NAMD - version 2.9 software packages, plus plotting programs (e.g., Excel on Windows, XMGrace on Unix/Mac) and text editors (e.g, Notepad on Windows, Emacs, vi on Unix, TextEdit on Mac) as described on the laptop requirements page. Be sure that all your software is installed and tested before you arrive at the workshop - there is no time on site for installation troubleshooting.II. Install Tutorials Texts and Files
Each tutorial consists of a text in pdf format, and computer files used in the tutorial. Be sure that you have the files you need each day of the tutorial sessions in place before you arrive at the workshop. Files by day of workshop tutorial session are listed below. It is easiest to follow the tutorials if files are placed in a 'Workshop' directory on the desktop.
Day 1 - Introduction to Protein Structure and Dynamics - Klaus Schulten
- Using VMD:
(pdf, 1.6M) (required tutorial files [.tar.gz, 44.9M], [.zip, 44.9M], Individual files) - NAMD Tutorial:
pdf for Unix/Mac, or pdf for Windows
required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms)
Day 2: Statistical Mechanics of Proteins; Force Field Parameterization - Emad Tajkhorshid
- Parameterizing a Novel Residue:
(pdf, 2.5M) (pdf for Linux, 2.5M)
(required tutorial files (all versions) [.tar.gz, 24.2M], [.zip, 24.2M], individual files (all versions)) - Topology File Tutorial:
(pdf, 4.4M ) (required tutorial files [.tar.gz, 11.2M], [.zip, 11.2M], individual files)
or,
- NAMD Tutorial:
(pdf for Unix/Mac, or pdf for Windows)
(required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms)) - Stretching Deca-alanine:
(pdf, 1.8M) (required tutorial files [.tar.gz, 5.3M], [.zip, 5.3M], individual files) - Other tutorials from the TCBG tutorials website (not printed, but will be supported)
Day 3: Computational Nano-Bio - Alek Aksimentiev
- Modeling Nanopores for Sequencing DNA
(pdf, 15M), (required tutorial files, [.tar.gz, 277M]) - Visualizing MD Results: Stretching dsDNA Mini Tutorial:
(pdf, 624k) (required tutorial files: reduced version [.tar.gz, 63M]; full version [.tar.gz, 613M]) - User-Defined Forces in NAMD:
(pdf, 4.3M ) (required tutorial files [.tar.gz, 306M], [.zip, 306M], individual files) - Introduction to MD Simulation of DNA-protein Systems:
(pdf, 4.4M) (required tutorial files [.tar.gz, 438M])
Day 4: Introduction to Bioinformatics - Zaida Luthey-Schulten
(See instructions here for configuring metadata for MultiSeq - needed for all tutorials)
- Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool:
(pdf, 4.6M) (required tutorial files [.tar.gz, 151M], [.zip, 151M], Individual files)
or,
- Expert Sequence Analysis
- Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA
complexes
(pdf, 6.4 MB) (required tutorial files [tar.gz, 268 MB]) - Evolution of Translation EF-Tu: tRNA: (pdf, 3.7 MB) (required tutorial files [tar.gz, 284 MB])
- Evolution of Translation: The Ribosome: (pdf, 1.3 MB) (required tutorial files [tar.gz, 41 MB])
- Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA
complexes
or,
- Dynamical Network Analysis:
(pdf, 4M) (required files [tar.gz, 192M]) (network analysis code [tar.gz, 27M])
or,
- Participants work on their own projects
Day 5: Simulating Membrane Proteins - Emad Tajkhorshid
- Membrane Proteins:
(pdf, 4.4M ) (reduced version of required tutorial files [.tar.gz, 10.2M], full version [.targ.z, 508M]) - Other tutorials from the TCBG tutorials website (not printed, but will be supported)
- GPU Tutorial (pdf, 443 KB) (required tutorial files [tar.gz, 1 GB])
- Open tutorial time